refactor: update Galaxy blueprints for MOSuite via this repo's github actions

.github/workflows/auto-format.yml

@@ -6,7 +6,7 @@ on:
 
 env:
   GH_TOKEN: ${{ github.token }}
-  TOOL_DOCKER: nciccbr/mosuite:v0.3.0
+  TOOL_DOCKER: nciccbr/mosuite:v0.4.0
 
 permissions:
   contents: write
@@ -21,24 +21,28 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.14"]
 
     steps:
-      - uses: actions/checkout@v4
-        if: github.event_name == 'pull_request'
+      - name: Generate a token
+        id: generate-token
+        uses: actions/create-github-app-token@v2
         with:
-          fetch-depth: 0
-          ref: ${{ github.head_ref }}
+          app-id: ${{ vars.CCBR_BOT_APP_ID }}
+          private-key: ${{ secrets.CCBR_BOT_PRIVATE_KEY }}
+          owner: ${{ github.repository_owner }}
 
-      - uses: actions/checkout@v4
-        if: github.event_name != 'pull_request'
+      - uses: actions/checkout@v7
         with:
+          token: ${{ steps.generate-token.outputs.token }}
           fetch-depth: 0
+          ref: ${{ github.event_name == 'pull_request' && github.head_ref ||
+            github.ref_name }}
 
       - name: git config
         run: |
-          git config --global user.name "github-actions[bot]"
-          git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git config --global user.name "CCBR-bot"
+          git config --global user.email "258092125+ccbr-bot@users.noreply.github.com"
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
@@ -52,17 +56,19 @@ jobs:
       - name: Format R code with air
         uses: rstudio/shiny-workflows/format-r-code@v1
 
-      # - name: update Galaxy blueprints
-      #   shell: Rscript {0}
-      #   run: |
-      #     source('inst/extdata/galaxy/galaxy.R') # TODO refactor
-      #     write_package_json_blueprints()
+      - name: update Galaxy blueprints
+        shell: Rscript {0}
+        container: ${{ env.TOOL_DOCKER }}
+        run: |
+          source('inst/extdata/galaxy/galaxy.R') # TODO refactor
+          write_package_json_blueprints()
 
       - name: Update Galaxy XML files
         run: |
           galaxysynth  "templates/2_blueprints/*.json" \
             --docker ${{ env.TOOL_DOCKER }} \
             --output templates/3_galaxy-tools
+
       - uses: quarto-dev/quarto-actions/setup@v2
         with:
           version: 1.4.515

templates/1_mosuite-templates/filter_counts.json

@@ -270,11 +270,11 @@
         {
             "key": "color_histogram_by_group",
             "displayName": "Color Histogram by Group",
-            "description": "Toggle to FALSE to label histogram by Sample Names. Toggle to TRUE to label histogram by the column you select in the \"Group Column Used to Color Histogram\" parameter (below). Default is FALSE.",
+            "description": "Toggle to FALSE to label histogram by Sample Names. Toggle to TRUE to label histogram by the column you select in the \"Group Column Used to Color Histogram\" parameter (below). Default is TRUE.",
             "paramType": "BOOLEAN",
             "paramGroup": "Histogram",
             "paramValues": null,
-            "defaultValue": "FALSE",
+            "defaultValue": "TRUE",
             "condition": null,
             "content": null,
             "objectPropertyReference": null

templates/1_mosuite-templates/normalize_counts.json

@@ -251,11 +251,11 @@
         {
             "key": "color_histogram_by_group",
             "displayName": "Color Histogram by Group",
-            "description": "Toggle to FALSE to label histogram by Sample Names. Toggle to TRUE to label histogram by the column you select in the \"Group Column Used to Color Histogram\" parameter (below). Default is FALSE.",
+            "description": "Toggle to FALSE to label histogram by Sample Names. Toggle to TRUE to label histogram by the column you select in the \"Group Column Used to Color Histogram\" parameter (below). Default is TRUE.",
             "paramType": "BOOLEAN",
             "paramGroup": "Histogram",
             "paramValues": null,
-            "defaultValue": "FALSE",
+            "defaultValue": "TRUE",
             "condition": null,
             "content": null,
             "objectPropertyReference": null

templates/2_blueprints/batch_correct_counts.json

@@ -53,9 +53,10 @@
     {
       "key": "label_colname",
       "displayName": "Labels Column",
-      "description": "The column from the sample metadata containing the sample labels as you wish them to appear in\nthe plots produced by this template. This can be the same Sample Names Column. However, you may desire different\nlabels to display on your figure (e.g. shorter labels are sometimes preferred on plots). In that case, select the\ncolumn with your preferred Labels here. The selected column should contain unique names for each sample. (Default:\n`NULL` -- `sample_id_colname` will be used.)\n",
+      "description": "The column from the sample metadata containing the sample labels as you wish them to appear in\nheatmap and PCA figures. This can be the same Sample Names Column. However, you may desire different labels to\ndisplay on your figures (e.g. shorter labels are sometimes preferred on plots). In that case, select the column with\nyour preferred Labels here. The selected column should contain unique names for each sample. Use `add_label_to_pca`to control whether these labels are displayed on the PCA plot.\n",
       "paramGroup": "Basic",
       "sourceDataset": "sample_metadata",
+      "defaultValue": "Label",
       "columnType": "ALL",
       "isMulti": null
     }
@@ -114,7 +115,7 @@
     {
       "key": "colors_for_plots",
       "displayName": "Colors for plots",
-      "description": "Colors for the PCA and histogram will be picked, in order, from this list.\nColors must either be names in `grDevices::colors()` or valid hex codes.\n",
+      "description": "Optional colors for PCA/histogram/heatmap plots. If `NULL`, colors are taken from\n`moo@analyses$colors[[group_colname]]`.\nColors must either be names in `grDevices::colors()` or valid hex codes.\nUnnamed colors are assigned by factor level order when the grouping column is a factor;\notherwise, they follow the order in which groups first appear in the metadata column. If more groups are present\nthan colors provided,\nsupplied colors are used first and additional colors are generated from the selected palette for the remaining\ngroups; random colors are used only if that palette returns fewer colors than the number of groups.\n",
       "paramType": "MULTISELECT",
       "paramGroup": "Visualization",
       "paramValues": [

templates/2_blueprints/diff_counts.json

@@ -42,7 +42,7 @@
     {
       "key": "covariates_colnames",
       "displayName": "Covariates Column(s)",
-      "description": "Columns to be used as covariates in linear modeling. Must include column from \"Contrast\nVariable\". Most commonly your covariate will be group and batch (if you have different batches in your data).\n",
+      "description": "The column name(s) from the sample metadata containing variable(s) of interest, such as\nphenotype. Most commonly this will be the same column selected for your Groups Column. Some experimental designs\nmay require that you add additional covariate columns here.\n",
       "paramGroup": "Basic",
       "sourceDataset": "Sample_Metadata",
       "columnType": "ALL",

templates/2_blueprints/filter_counts.json

@@ -43,9 +43,10 @@
     {
       "key": "label_colname",
       "displayName": "Labels Column",
-      "description": "The column from the sample metadata containing the sample labels as you wish them to appear in\nthe plots produced by this template. This can be the same Sample Names Column. However, you may desire different\nlabels to display on your figure (e.g. shorter labels are sometimes preferred on plots). In that case, select the\ncolumn with your preferred Labels here. The selected column should contain unique names for each sample. (Default:\n`NULL` -- `sample_id_colname` will be used.)\n",
+      "description": "The column from the sample metadata containing the sample labels as you wish them to appear in\nheatmap and PCA figures. This can be the same Sample Names Column. However, you may desire different labels to\ndisplay on your figures (e.g. shorter labels are sometimes preferred on plots). In that case, select the column with\nyour preferred Labels here. The selected column should contain unique names for each sample. Use `add_label_to_pca`to control whether these labels are displayed on the PCA plot.\n",
       "paramGroup": "Basic",
       "sourceDataset": "Sample_Metadata",
+      "defaultValue": "Label",
       "columnType": "ALL",
       "isMulti": null
     }
@@ -104,7 +105,7 @@
     {
       "key": "minimum_count_value_to_be_considered_nonzero",
       "displayName": "Minimum Count Value to be Considered Nonzero",
-      "description": "Minimum count value to be considered non-zero for a sample\n",
+      "description": "Minimum value in the selected filtering table required for a\nsample to be considered nonzero. If `use_cpm_counts_to_filter` is `TRUE`, this threshold is applied to CPM values.\nIf `use_cpm_counts_to_filter` is `FALSE`, this threshold is applied directly to the selected `count_type` table.\n",
       "paramType": "NUMBER",
       "paramGroup": "Filtering",
       "paramValues": null,
@@ -116,7 +117,7 @@
     {
       "key": "minimum_number_of_samples_with_nonzero_counts_in_total",
       "displayName": "Minimum Number of Samples with Nonzero Counts in Total",
-      "description": "Minimum number of samples (total) with non-zero counts\n",
+      "description": "Minimum number of samples in total that must meet the\n`minimum_count_value_to_be_considered_nonzero` threshold for a feature to be kept.\n",
       "paramType": "NUMBER",
       "paramGroup": "Filtering",
       "paramValues": null,
@@ -128,7 +129,7 @@
     {
       "key": "use_group_based_filtering",
       "displayName": "Use Group-Based Filtering",
-      "description": "If TRUE, only keeps features (e.g. genes) that have at least a certain number of\nsamples with nonzero CPM counts in at least one group\n",
+      "description": "If TRUE, only keeps features (e.g. genes) that have at least a certain number of\nsamples passing the threshold in at least one group\n",
       "paramType": "BOOLEAN",
       "paramGroup": "Filtering",
       "paramValues": null,
@@ -140,7 +141,7 @@
     {
       "key": "minimum_number_of_samples_with_nonzero_counts_in_a_group",
       "displayName": "Minimum Number of Samples with Nonzero Counts in a Group",
-      "description": "Only keeps genes that have at least this number of\nsamples with nonzero CPM counts in at least one group\n",
+      "description": "Only keeps genes that have at least this number of\nsamples meeting the threshold in at least one group\n",
       "paramType": "NUMBER",
       "paramGroup": "Filtering",
       "paramValues": null,
@@ -198,15 +199,15 @@
       "paramType": "NUMBER",
       "paramGroup": "PCA",
       "paramValues": null,
-      "defaultValue": 1,
+      "defaultValue": 5,
       "condition": null,
       "content": null,
       "objectPropertyReference": null
     },
     {
       "key": "add_label_to_pca",
       "displayName": "Add Labels to PCA",
-      "description": "label points on the PCA plot\n",
+      "description": "If `TRUE`, display labels from `label_colname` on PCA points. If `FALSE`, the PCA plot uses\nunlabeled points while heatmap labels still use `label_colname`.\n",
       "paramType": "BOOLEAN",
       "paramGroup": "PCA",
       "paramValues": null,
@@ -266,11 +267,11 @@
     {
       "key": "color_histogram_by_group",
       "displayName": "Color Histogram by Group",
-      "description": "Set to FALSE to label histogram by Sample Names, or set to TRUE to label histogram by\nthe column you select in the \"Group Column Used to Color Histogram\" parameter (below). Default is FALSE.\n",
+      "description": "Set to FALSE to label histogram by Sample Names, or set to TRUE to label histogram by\nthe column you select in the \"Group Column Used to Color Histogram\" parameter (below). Default is TRUE.\n",
       "paramType": "BOOLEAN",
       "paramGroup": "Histogram",
       "paramValues": null,
-      "defaultValue": false,
+      "defaultValue": true,
       "condition": null,
       "content": null,
       "objectPropertyReference": null
@@ -314,11 +315,10 @@
     {
       "key": "legend_font_size_for_histogram",
       "displayName": "Legend Font Size for Histogram",
-      "description": "legend font size for the histogram plot\n",
+      "description": "legend font size for the histogram plot.\nIf `NULL`, the size is scaled automatically.\n",
       "paramType": "NUMBER",
       "paramGroup": "Histogram",
       "paramValues": null,
-      "defaultValue": 10,
       "condition": null,
       "content": null,
       "objectPropertyReference": null
@@ -356,7 +356,7 @@
     {
       "key": "colors_for_plots",
       "displayName": "Colors for Plots",
-      "description": "Colors for the PCA and histogram will be picked, in order, from this list.\nColors must either be names in `grDevices::colors()` or valid hex codes.\n",
+      "description": "Optional colors for PCA/histogram/heatmap plots. If `NULL`, colors are taken from\n`moo@analyses$colors[[group_colname]]`.\nColors must either be names in `grDevices::colors()` or valid hex codes.\nUnnamed colors are assigned by factor level order when the grouping column is a factor;\notherwise, they follow the order in which groups first appear in the metadata column. If more groups are present\nthan colors provided,\nsupplied colors are used first and additional colors are generated from the selected palette for the remaining\ngroups; random colors are used only if that palette returns fewer colors than the number of groups.\n",
       "paramType": "MULTISELECT",
       "paramGroup": "Visualization",
       "paramValues": [

templates/2_blueprints/normalize_counts.json

@@ -43,9 +43,10 @@
     {
       "key": "label_colname",
       "displayName": "Labels Column",
-      "description": "The column from the sample metadata containing the sample labels as you wish them to appear in\nthe plots produced by this template. This can be the same Sample Names Column. However, you may desire different\nlabels to display on your figure (e.g. shorter labels are sometimes preferred on plots). In that case, select the\ncolumn with your preferred Labels here. The selected column should contain unique names for each sample. (Default:\n`NULL` -- `sample_id_colname` will be used.)\n",
+      "description": "The column from the sample metadata containing the sample labels as you wish them to appear in\nheatmap and PCA figures. This can be the same Sample Names Column. However, you may desire different labels to\ndisplay on your figures (e.g. shorter labels are sometimes preferred on plots). In that case, select the column with\nyour preferred Labels here. The selected column should contain unique names for each sample. Use `add_label_to_pca`to control whether these labels are displayed on the PCA plot.\n",
       "paramGroup": "Basic",
       "sourceDataset": "Sample_Metadata",
+      "defaultValue": "Label",
       "columnType": "ALL",
       "isMulti": null
     }
@@ -145,7 +146,7 @@
     {
       "key": "add_label_to_pca",
       "displayName": "Add Labels to PCA",
-      "description": "label points on the PCA plot\n",
+      "description": "If `TRUE`, display labels from `label_colname` on PCA points. If `FALSE`, the PCA plot uses\nunlabeled points while heatmap labels still use `label_colname`.\n",
       "paramType": "BOOLEAN",
       "paramGroup": "PCA",
       "paramValues": null,
@@ -239,15 +240,15 @@
       "paramType": "NUMBER",
       "paramGroup": "PCA",
       "paramValues": null,
-      "defaultValue": 8,
+      "defaultValue": 5,
       "condition": null,
       "content": null,
       "objectPropertyReference": null
     },
     {
       "key": "color_histogram_by_group",
       "displayName": "Color Histogram by Group",
-      "description": "Set to FALSE to label histogram by Sample Names, or set to TRUE to label histogram by\nthe column you select in the \"Group Column Used to Color Histogram\" parameter (below). Default is FALSE.\n",
+      "description": "Set to FALSE to label histogram by Sample Names, or set to TRUE to label histogram by\nthe column you select in the \"Group Column Used to Color Histogram\" parameter (below). Default is TRUE.\n",
       "paramType": "BOOLEAN",
       "paramGroup": "Histogram",
       "paramValues": null,
@@ -295,11 +296,10 @@
     {
       "key": "legend_font_size_for_histogram",
       "displayName": "Legend Font Size for Histogram",
-      "description": "legend font size for the histogram plot\n",
+      "description": "legend font size for the histogram plot.\nIf `NULL`, the size is scaled automatically.\n",
       "paramType": "NUMBER",
       "paramGroup": "Histogram",
       "paramValues": null,
-      "defaultValue": 10,
       "condition": null,
       "content": null,
       "objectPropertyReference": null
@@ -337,7 +337,7 @@
     {
       "key": "colors_for_plots",
       "displayName": "Colors for Plots",
-      "description": "Colors for the PCA and histogram will be picked, in order, from this list.\nColors must either be names in `grDevices::colors()` or valid hex codes.\n",
+      "description": "Optional colors for PCA/histogram/heatmap plots. If `NULL`, colors are taken from\n`moo@analyses$colors[[group_colname]]`.\nColors must either be names in `grDevices::colors()` or valid hex codes.\nUnnamed colors are assigned by factor level order when the grouping column is a factor;\notherwise, they follow the order in which groups first appear in the metadata column. If more groups are present\nthan colors provided,\nsupplied colors are used first and additional colors are generated from the selected palette for the remaining\ngroups; random colors are used only if that palette returns fewer colors than the number of groups.\n",
       "paramType": "MULTISELECT",
       "paramGroup": "Visualization",
       "paramValues": [

templates/2_blueprints/plot_expr_heatmap.json

@@ -399,7 +399,7 @@
     {
       "key": "group_colors",
       "displayName": "Group Colors",
-      "description": "Set group annotation colors.\n",
+      "description": "Set group annotation colors.",
       "paramType": "MULTISELECT",
       "paramGroup": "Annotation",
       "paramValues": [
@@ -416,7 +416,7 @@
         "#FFA500",
         "#878500"
       ],
-      "defaultValue": ["#5954d6", "#e1562c", "#b80058", "#00c6f8", "#d163e6", "#00a76c", "#ff9287", "#008cf9", "#006e00", "#796880", "#FFA500", "#878500"],
+      "defaultValue": null,
       "condition": null,
       "content": null,
       "objectPropertyReference": null